4II3

Crystal structure of S. pombe Ubiquitin activating enzyme 1 (Uba1) in complex with ubiquitin and ATP/Mg

Structural Biology Knowledgebase: 4II3 SBKB.org


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.283
  • R-Value Work: 0.239

wwPDB Validation Full Report


Literature

Macromolecules
Sequence Display for 4II3

Classification: LIGASE

Total Structure Weight: 246522.27

Macromolecule Entities
Molecule Chains Length Organism Details
Ubiquitin-activating enzyme E1 1 A, C 1001 Schizosaccharomyces pombe EC#: 6.2.1.45 IUBMB
Fragment: Uba1, UNP residues 13-1012
Gene Name(s): ptr3 SPBC1604.21c SPBC211.09
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG
Ubiquitin-60S ribosomal protein L40 B, D 96 Schizosaccharomyces pombe Fragment: UNP residues 1-76
Gene Name(s): uep1 ubi2 SPAC1805.12c
Metabolic Pathways
Maps:       
Reactions:
ESCHER  BiGG

Small Molecules
Ligands 3 Unique
ID Chains Name / Formula / InChI Key 2D Diagram 3D Interactions
ATP
Query on ATP

A, C ADENOSINE-5'-TRIPHOSPHATE
C10 H16 N5 O13 P3
ZKHQWZAMYRWXGA-KQYNXXCUSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
CA
Query on CA

A, C CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)
MG
Query on MG

A, C MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
Ligand Explorer
 
Binding Pocket (JSmol)
 
Electron Density (JSmol)

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.9 Å
  • R-Value Free: 0.283
  • R-Value Work: 0.239
  • Space Group: P 21 21 2
  • Electron Density Server: EDS EDS

Unit Cell:

Length (Å) Angle (°)
a = 180.50 α = 90.00
b = 113.30 β = 90.00
c = 126.60 γ = 90.00

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History

Deposition Data

  • Deposited Date: 2012-12-19
  • Released Date: 2013-02-13
  • Deposition author(s): Olsen, S.K., Lima, C.D.

Revision History

  • 2013-03-27
    Type: Citation | Details: Citation update